DAP method: Difference between revisions
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Revision as of 08:50, 4 June 2008
Blastp
- FASTA SEQUENCE FROM NCBI ENTREZ protein = 2IJZ_A
- Origin of query sequence = Pseudomonas aeruginosa
>gi|119390187|pdb|2IJZ|A Chain A, Crystal Structure Of Aminopeptidase RAELNQGLIDFLKASPTPFHATASLARRLEAAGYRRLDERDAWHTETGGRYYVTRNDSSLIAIRLGRRSP LESGFRLVGAHTDSPCLRVKPNPEIARNGFLQLGVEVYGGALFAPWFDRDLSLAGRVTFRANGKLESR LVDFRKAIAVIPNLNIHLNRAANEGWPINAQNELPPIIAQLAPGEAADFRLLLDEQLLREHGITADVVLDYE LSFYDTQSAAVVGLNDEFIAGARLDNLLSCHAGLEALLNAEGDENCILVCTDHEEVGSCSHCGADGPFLE QVLRRLLPEGDAFSRAIQRSLLVSADNAHGVHPNYADRHDANHGPALNGGPVIKINSNQRYATNSETA GFFRHLCQDSEVPVQSFVTRSDMGCGSTIGPITASQVGVRTVDIGLPTFAMHSIRELAGSHDLAHLVKVLGA FYASSELP
- Performed blastp search against non-redundant (nr) databases which was provided on the CD provided. Query sequences used was Pseudomonas Aeruginosa chain A crystal structure of asparytl aminopeptidase.
- Initial sequence alignment was performed using ClustalX and edited to reduce gapping in the alignment and final multiple sequence alignment was again performed with 38 sequences.
- Treeview32 software was used to view phylogenetic tree produced from multiple sequence alignment and a bootstrapped N-J tree was produced using Clustalx for branches reliability indications.
As mentioned in the methods and website :
C:\blast\blastall -p blastp -d C:\blast\databases\nr -i yourfile.fasta -o usefuloutputname.html
Obtained fastaformat files
C:\blast\fastacmd -d C:\blast\databases\nr -i filewith_img_numbers -o C:\newsequences.fasta
Inputs used for obtaining fastaformat files:
pdb|2IJZ|A ref|YP_789908.1| ref|YP_261475.1| ref|ZP_00416764.1| ref|NP_743887.1| ref|NP_793647.1| ref|YP_607123.1| ref|YP_958321.1| ref|ZP_01894798.1| ref|ZP_01166960.1| ref|ZP_01738318.1| ref|YP_436072.1| ref|ZP_01462550.1| ref|YP_630602.1| ref|YP_001615044.1| ref|YP_747571.1| ref|YP_113441.1| ref|XP_001751765.1| ref|XP_001641062.1| ref|XP_713998.1| gb|AAM61631.1| ref|XP_365906.1| ref|XP_843934.1| ref|NP_001045513.1| ref|XP_001566576.1| ref|XP_001877081.1| gb|ACC64563.1| ref|XP_001492028.1| ref|NP_001039417.1| ref|YP_833603.1| ref|NP_036232.2| ref|NP_001012937.1| ref|NP_001104301.1| gb|EDL75426.1| ref|NP_001085525.1| ref|XP_462175.1| ref|NP_956447.1|
Changed headings in every single obtained fasta sequences into organism names only, e.g :
From
>gi|116051260|ref|YP_789908.1| putative aminopeptidase 2 [Pseudomonas aeruginosa UCBPP-PA14]
MRAELNQGLIDFLKASPTPFHATASLARRLEAAGYRRLDERDAWHTEAGGRYYVTRNDSSLIAIRLGRRSPLESGFRLVG
AHTDSPCLRVKPNPEIARNGFLQLGVEVYGGALFAPWFDRDLSLAGRVTFRANGKLESRLVDFRKAIAVIPNLAIHLNRA
ANEGWPINAQNELPPIIAQLAPGEAADFRLLLDEQLLREHGITADVVLDYELSFYDTQSAAVVGLNDEFIAGARLDNLLS
CHAGLEALLNAEGDENCILVCTDHEEVGSCSHCGADGPFLEQVLRRLLPEGDAFSRAIQRSLLVSADNAHGVHPNYADK
DANHGPALNGGPVIKINSNQRYATNSETAGFFRHLCQDSEVPVQSFVTRSDMGCGSTIGPITASQVGVRTVDIGLPTFAM
HSIRELAGSHDLAHLVKVLGAFYASSELP
To
>Pseudomonas_aeruginosa
MRAELNQGLIDFLKASPTPFHATASLARRLEAAGYRRLDERDAWHTEAGGRYYVTRNDSSLIAIRLGRRSPLESGFRLVG
AHTDSPCLRVKPNPEIARNGFLQLGVEVYGGALFAPWFDRDLSLAGRVTFRANGKLESRLVDFRKAIAVIPNLAIHLNRA
ANEGWPINAQNELPPIIAQLAPGEAADFRLLLDEQLLREHGITADVVLDYELSFYDTQSAAVVGLNDEFIAGARLDNLLS
CHAGLEALLNAEGDENCILVCTDHEEVGSCSHCGADGPFLEQVLRRLLPEGDAFSRAIQRSLLVSADNAHGVHPNYADK
DANHGPALNGGPVIKINSNQRYATNSETAGFFRHLCQDSEVPVQSFVTRSDMGCGSTIGPITASQVGVRTVDIGLPTFAM
HSIRELAGSHDLAHLVKVLGAFYASSELP
saved into a new file organismnames.fasta
CLUSTALX
Used ClustalX 1.83multiple alignment software tool to align C:\3rdplaceoutnames.fasta. Output format options was changed to NODE before bootstrapping, this is performed in order see reliability of branches in treeview.
Example:
Conserved regions (*) of >gi|119390187|pdb|2IJZ|A Chain A, Crystal Structure Of Aminopeptidase was noted for structural analysis.
Output obtained : .aln file (alignment) and .dnd file (output guide tree)
Bootstrapping : .phb file obtained
Treeview
Used Treeview to visualize Phylogenetic tree:
- Radial Tree
- Rectangular Cladogram
The results from the blast search were then screened and a selection was of these results were used for a multiple sequence alignment using ClustalX. This result was boostrapped and these values checked and more sequences were added to improve the resolution of specific branches. A bootstrapped phylogram was produces, aswell as a radial tree.